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Scholars Day 2006, Wednesday, April 12

Visualization of Molecular Simulations by VMD

The use of VMD (Visual Molecular Dynamics) software for visualizing molecular simulations from a Web interface is described. Results from molecular simulation calculations are animated as a series of snapshots, each of which shows the positions and types of all atoms comprising the molecular system being simulated. Data for these snapshots are generated on a linux workstation and are sent to a PC on which VMD has been installed, and animated by VMD, either subsequently or as the simulation is being performed. Issues related to set-up and data sharing between different machines are described, as are a series of features added to the Web interface. For illustration, normal modes from the recently developed trajectory averaged normal coordinate analysis method are visualized.

Presenter: Subin Sindurakar (Undergraduate Student)
Topic: Computational Science
Location: 204 Holmes
Time: 9 am (Session I)